<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=Content-Type content="text/html; charset=iso-8859-1">
<META content="MSHTML 6.00.2734.1600" name=GENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=#ffffff>
<DIV><FONT face=Arial size=2>Hello,</FONT></DIV>
<DIV><FONT face=Arial size=2>I'm trying to run a simulation of a protein
(1PID.pdb) against a model surface (mica or HOPG) for which I also have the .pdb
file. Could someone explain to me how to incorporate the protein and the
surface together in a model in order to do mdrun. Which Gromacs
commands do this? So far I've been trying to build the model by
editing the text files manually, but that's really bad, and I haven't been able
to find this information in the manual.</FONT></DIV>
<DIV><FONT face=Arial size=2>Any hints/explanations would be much
appreciated.</FONT></DIV>
<DIV><FONT face=Arial size=2>Thanks</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Vanja P.</FONT></DIV>
<DIV><FONT face=Arial size=2>University of Toronto</FONT></DIV></BODY></HTML>